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A Comparative Study for the Accuracy of Three Molecular Docking Programs Using HIV-1 Protease Inhibitors as a Model
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Flexible molecular docking is a computational method of structure-based drug design to evaluate binding interactions between receptor and ligand and identify the ligand conformation within the receptor pocket. Currently, various molecular docking programs are extensively applied; therefore, realizing accuracy and performance of the various docking programs could have a significant value. In this comparative study, the performance and accuracy of three widely used non-commercial docking software (AutoDock Vina, 1-Click Docking, and UCSF DOCK) was evaluated through investigations of the predicted binding affinity and binding conformation of the same set of small molecules (HIV-1 protease inhibitors) and a protein target HIV-1 protease enzyme. The tested sets are composed of eight receptor-ligand complexes with high resolution crystal structures downloaded from Protein Data Bank website. Molecular dockings were applied between approved HIV-1 protease inhibitors and the HIV-1 protease using AutoDock Vina, 1-Click Docking, and DOCK6. Then, docking poses of the top-ranked solution was realized using UCSF Chimera. Furthermore, Pearson correlation coefficient (r) and coefficient of determination (r2) between the experimental results and the top scored docking results of each program were calculated using Graphpad prism V9.2. After comparing saquinavir top scored binding poses of each docking program with the crystal structure, various conformational changes were observed. Moreover, according to the relative comparison between the top ranked calculated ?Gbinding values against the experimental results, r2 value of AutoDock Vina, 1-Click Docking, and DOCK6 were 0.65, 0.41, and 0.005, respectively. The outcome of this study shows that the top scored binding free energy could not produce the best pose prediction. In addition, AutoDock Vina results have the highest correlation with the experimental results.

 

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Publication Date
Thu Sep 01 2022
Journal Name
Archives Of Razi Institute
Effects of Avena sativa and Glycyrrhiza glabra Leaves Extracts on Immune Responses in Serum Cytokine and Liver Enzyme Levels in NIH Mice
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In addition to their high quantities of active chemicals, medicinal plants are well-known for their pharmacological qualities, which include immunological modulation. T Consequently, this study aimed to examine the effects of Avena sativa and Glycyrrhiza glabra leaf extracts on immunological responses as measured by blood cytokine and liver enzyme levels. The phytochemical analysis of Avena sativa crude leaf extracts revealed the presence of alkaloids,flavonoids, tannins, phenolic compounds, and saponins but the absence of resins and violet oils. On the other hand, violet oils, flavonoids, tannins, saponins, and glycosides were detected in significant concentration in Glycyrrhiza glabra ethanolic extract, although resins and phenolic compou

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Publication Date
Tue Mar 08 2016
Journal Name
Ibn Al-haitham Jour. For Pure & Appl. Sci.
Synthesis, Characterization and Spectral Studies of Y(III), La(II) and Rh(III) Complexes with 2,4-dimethyl-6-(4-nitro-phenylazo)- Phenol
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Transition metal complexes of Y(III), La(III) and Rh(III) with azo dye 2,4-dimethyl-6- (4-nitro-phenylazo)-phenol derived from 4-nitroaniline and 2,4-dimethylphenol were synthesized. Characterization of these compounds has been done on the basis of elemental analysis, electronic data, FT-IR,UV-Vis and 1HNMR, as well as conductivity measurements. The nature of the complexes formed were studies following the mole ratio and continuous variation methods, Beer's law obeyed over a concentration range (1x10-4- 3x10-4). High molar absorbtivity of the complex solutions were observed. From the analytical data, the stoichiomerty of the complexes has been found to be 1:3 (Metal:ligand). On the basis of Physicochemical data octahedral geometries were as

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Publication Date
Tue Jan 09 2018
Journal Name
Iraqi Journal Of Cancer And Medical Genetics
Photodynamic Action of low power He-Ne laser on photosensitized human Hep-2 and AMN3 cell lines with Hematoporphyrin derivative in vitro
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Photodynamic Action (PDA) by using appropriate wavelength of irradiation conjugated with porphyrin derivatives is a powerful mechanism of tumor destruction. Hematoporphyrin derivative has been shown to selectively localize in neoplastic cells and then cause destruction of them by generation of singlet oxygen when activated by low power He-Ne laser. Light which used in this study has been emitting from this laser has a wavelength equal to 632.8 nm (red light). Doses of laser had been varied from 3.6 J/cm2 to 14.4 J/cm2 . The beam of laser adjusted with a modified tissue culture plate. Cell lines had exposed to Hematoporphyrin D (HpD) for 24 hours before Laser exposure, their concentrations were varied from 5 µg/ml to 80 µg/ml. Resu

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Publication Date
Mon Aug 19 2024
Journal Name
Chemical Papers
In vitro and in silico evaluation of 4'-hydroxy-[1,1'-biphenyl]-4-carbohydrazide Schiff base and oxadiazole derivatives targeting EGFR allosteric site
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Publication Date
Mon Oct 31 2016
Journal Name
International Journal Of Advanced Research
SINGLE NUCLEOTIDE POLYMORPHISMS (SNPS) IN EXON 3 AND 7 OF ESTROGEN RECEPTOR BETA (ESR2) GENE IN WOMEN WITH BREAST CANCER FROM IRAQ.
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This study was aimed to determine the mutations and single nucleotide polymorphisms (SNPs) in exon 3 and 7 of estrogen receptor beta (ESR2) gene in women with breast cancer from Iraq. Different samples (blood, fresh tissue with blood from same patient, and formalin fixed paraffin embedded, FFPE) were collected from women with breast cancer. Molecular analysis exon 3 and 7 in ESR2 has been studied by using PCR. It was found exon 3 and 7 in ESR2 were revealed as a single band with size 151 and 157 bp, respectively. There was no SNP in exon 3 has been identified. While three novel polymorphisms (ACT, AGG and GCA) were detected in exon 7, the type of those polymorphisms deletion for ACT and AGG while substitution polymorphism for GCA. From this

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Publication Date
Wed May 19 2010
Journal Name
College Of Science – University Of Babylon
Synthesis and Characterisation of Cu(II) ,Co(II) ,Ni(II) and Zn(II) Complexes Derived from Acetylacetone and P–Amino benzoic acid
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Publication Date
Tue Sep 28 2021
Journal Name
Journal Of Physical Education
Youth and Sports Forums’ Administration and Their Relationship with Baghdad’s Youth and Sport Directorates Forum Organizational Culture from Workers’ Point of View
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The study aimed at identifying youth and sport forums from planning and leadership point of view and their relation with organizational culture. The researchers used the descriptive method on (140) worker in Baghdad youth and sport forums. A scale was designed for measuring planning and leadership in youth and sport forums as well as designing a scale for measuring organizational culture. After the application of the main experiment, the results showed that both youth and sport forum administration scale and organizational culture scale are appropriate to the study community. Finally the researchers recommended using these scales by workers in youth and sport forums and involving administration mangers in periodical training courses

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Publication Date
Tue Jul 22 2025
Journal Name
Journal Of Baghdad College Of Dentistry
Dental caries, Mutans Streptococci, Lactobacilli and salivary status of type1 diabetic mellitus patients aged 18-22 years in relation to Glycated Haemoglobin
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Background: diabetic mellitus is one of the serious systemic diseases that may cause general systemic changes, which may be reflected in the oral cavity. The aims of this study were to assess the severity of dental caries, Mutans Streptococci and Lactobacilli in addition to flow rate and pH among uncontrolled and controlled diabetic groups in comparison with non-diabetic control group. Materials and Methods: Study groups consisted of 25 uncontrolled diabetic patients (HbA1c > 7), 25 controlled diabetic patients (HbA1c ? 7), in addition to 25 non-diabetic healthy looking individuals. Their age was (18-22) years from both genders. The diagnosis and recording of dental caries was according to severity of dental caries lesion through the applic

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Publication Date
Tue Jan 01 2019
Journal Name
Journal Of Southwest Jiaotong University
Inclined Magnetic Field of Non-uniform and Porous Medium Channel on Couple Stress Peristaltic Flow and application in medical treatment (Knee Arthritis)
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The present study analyzes the effect of couple stress fluid (CSF) with the activity of connected inclined magnetic field (IMF) of a non-uniform channel (NUC) through a porous medium (PM), taking into account the sliding speed effect on channel walls and the effect of nonlinear particle size, applying long wavelength and low Reynolds count estimates. The mathematical expressions of axial velocity, stream function, mechanical effect and increase in pressure have been analytically determined. The effect of the physical parameter is included in the present model in the computational results. The results of this algorithm have been presented in chart form by applying the mathematical program.

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Publication Date
Sun Sep 27 2020
Journal Name
Iraqi National Journal Of Nursing Specialties
Effectiveness of an Education Program on Nursing Staffs' Knowledge about Infection Control Measures at Intensive Care Unit in Al-Diwaniya Teaching Hospital
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Objectives: To determine the effectiveness of the educational program on nursing staff knowledge about infection control measures at the Intensive Care Unit in Al-Diwaniya Teaching Hospital.

Methodology: A pre-experimental design (one group design: pre-test and post-test) was used. This study was conducted in Al-Diwaniya Teaching Hospital for the period from ( 20th February to 5th March, 2020) on a non-probability (purposive) sample consisting of (25 nurses) working in ICU. A questionnaire was built as a data collection tool and consisted of two parts:

First part: The demographic characteristics of the nursing staff (age, gender, level of education, years of experien

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